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Sample GSM152163 Query DataSets for GSM152163
Status Public on Jul 30, 2007
Title HMEC DEP-5 mcg/ml 1432059024_H
Sample type RNA
 
Source name HMEC
Organism Homo sapiens
Characteristics Confluent HMEC in 6-well plates were treated in triplicate by DEP-5 mcg/ml for 4 hours. Cells were harvested and cytoplasmic RNA was isolated by RNAeasykit (Qiagen) and analyzed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) to assess RNA integrity. Biotin-labeled cRNA was synthesized by the Ambion Total prep RNA amplification kit. cRNA was quantified and normalized to 77 ng/mcl, and then 850 ng was hybridized to Beadchips (Beadchip 8X1 from Illumina, Inc. San Diego, CA) that contains probes for ~23,000 transcripts. The hybridized Beadchips were scanned by Illumina BeadScan confocal scanner and analyzed by Illumina's BeadStudio version 1.5.1.3. cRNA synthesis, hybridization and scanning was performed at the Southern California Genotyping Consortium's Illumina BeadLab located at UCLA. The microarray data was normalized and analyzed by Illumina Inc. BeadStudio software, version 1.5.0.34 (Illumina, Inc. San Diego, CA)
Extracted molecule total RNA
Extraction protocol cytoplasmic RNA was isolated by RNAeasykit (Qiagen) and analyzed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) to assess RNA integrity.
Label Biotin Streptavidin-Cy3
Label protocol Biotin-labeled cRNA was synthesized by the Ambion Total prep RNA amplification kit. cRNA was quantified and normalized to 77 ng/mcl
 
Hybridization protocol 850 ng was hybridized to Beadchips (Beadchip 8X1 from Illumina, Inc. San Diego, CA) that contains probes for ~23,000 transcripts.
Scan protocol The hybridized Beadchips were scanned by Illumina BeadScan confocal scanner and analyzed by Illumina's BeadStudio version 1.5.1.3. cRNA synthesis, hybridization and scanning was performed at the Southern California Genotyping Consortium's Illumina BeadLab located at UCLA.
Description Replicate of HMEC DEP-5 mcg/ml
Data processing The data were analyzed with Illumina Inc. BeadStudio version 1.5.0.34 and normalized by rank invariant method.
 
Submission date Dec 20, 2006
Last update date Jul 30, 2007
Contact name Leslie Ingram-drake
E-mail(s) lingram@mednet.ucla.edu
Phone 310-794-9036
Fax 310-794-7345
URL http://www.mednet.ucla.edu
Organization name UCLA
Department Medicine/MIMG/Human Genetics
Street address 47-123 CHS
City Los Angeles
State/province CA
ZIP/Postal code 90095-1359
Country USA
 
Platform ID GPL2700
Series (1)
GSE6584 HMEC nine-condition expression profiling

Data table header descriptions
ID_REF TargetID
VALUE rank invariant normalized average intensity signal across probe specific beads
Detection_score 1-p-value computed from the background model characterizing the chance that the target sequence signal was distinguishable from the negative controls

Data table
ID_REF VALUE Detection_score
GI_41350203-S 3511.00 1.00
GI_25453471-A 34602.40 1.00
GI_19923986-S 4.60 0.66
GI_37543909-S 13.10 0.81
GI_42741672-S 558.40 1.00
GI_19743802-S 31.00 0.94
GI_38016936-S 42.20 0.97
GI_16118224-S -10.60 0.23
GI_34330167-S -2.90 0.46
GI_34878734-I -5.50 0.37
GI_6912325-S 132.20 0.99
GI_24041019-A 1290.20 1.00
GI_31341671-S 8.90 0.74
GI_4502864-S 1.90 0.60
GI_38570141-S 23.10 0.91
GI_11038629-I 11.00 0.77
GI_10190745-S 503.60 1.00
GI_8922791-S 361.40 1.00
GI_41151283-S -12.80 0.18
GI_31559820-S -0.60 0.52

Total number of rows: 24354

Table truncated, full table size 601 Kbytes.




Supplementary file Size Download File type/resource
GSM152163.txt.gz 372.3 Kb (ftp)(http) TXT
Processed data included within Sample table

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